Single cell type - PDS5B - The Human Protein Atlas

PDS5B

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GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	PDS5B
Gene descriptionⁱ Full gene name according to HGNC.	PDS5 cohesin associated factor B
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Neurons - Neuronal signaling (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Cell type enhanced (Inhibitory neurons, Excitatory neurons)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.37
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Low cell type specificity
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types RNA single cell type specificity: Cell type enhanced (Inhibitory neurons, Excitatory neurons)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

PDS5B is part of cluster 69 Neurons - Neuronal signaling with confidenceⁱ 1
331 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
RUNX1T1	RUNX1 partner transcriptional co-repressor 1	0.5887	69
TSHZ3	Teashirt zinc finger homeobox 3	0.5870	8
ARHGAP20	Rho GTPase activating protein 20	0.5799	8
VPS13B	Vacuolar protein sorting 13 homolog B	0.5481	69
TRO	Trophinin	0.5461	9
TRHDE	Thyrotropin releasing hormone degrading enzyme	0.5228	69
NRXN3	Neurexin 3	0.5110	69
RAB6C	RAB6C, member RAS oncogene family	0.5052	9
SHISA6	Shisa family member 6	0.5031	69
CACNA1D	Calcium voltage-gated channel subunit alpha1 D	0.4971	69
GLI1	GLI family zinc finger 1	0.4955	9
NBEA	Neurobeachin	0.4948	69
PNMA6F	PNMA family member 6F	0.4947	69
CDH9	Cadherin 9	0.4928	69
TRPC6	Transient receptor potential cation channel subfamily C member 6	0.4927	69

IMMUNE CELLS

PDS5B is part of cluster 35 Neutrophils - Protein binding with confidenceⁱ 0.87
504 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
ZNF320	Zinc finger protein 320	0.9762	35
ITCH	Itchy E3 ubiquitin protein ligase	0.9524	35
SPPL3	Signal peptide peptidase like 3	0.9524	35
CNNM2	Cyclin and CBS domain divalent metal cation transport mediator 2	0.9524	35
POM121C	POM121 transmembrane nucleoporin C	0.9286	35
PHF2	PHD finger protein 2	0.9286	35
SETD5	SET domain containing 5	0.9286	24
FNDC3A	Fibronectin type III domain containing 3A	0.9286	35
TNFSF4	TNF superfamily member 4	0.9048	35
SENP1	SUMO specific peptidase 1	0.9048	5
ATOSA	Atos homolog A	0.9048	24
DHCR7	7-dehydrocholesterol reductase	0.8810	24
SLC38A2	Solute carrier family 38 member 2	0.8571	30
HSF2BP	Heat shock transcription factor 2 binding protein	0.8571	24
DDX55	DEAD-box helicase 55	0.8571	30

Adipocytes	46.4 nTPM
Adipose tissue	57.5 nTPM
Breast	35.3 nTPM

Alveolar cells type 1	27.6 nTPM
Lung	27.6 nTPM

Alveolar cells type 2	34.9 nTPM
Lung	34.9 nTPM

Astrocytes	82.4 nTPM
Brain	82.4 nTPM

B-cells	34.0 nTPM
Salivary gland	54.4 nTPM
Adipose tissue	46.1 nTPM
PBMC	44.6 nTPM
Liver	43.5 nTPM
Lymph node	41.7 nTPM
Bone marrow	38.6 nTPM
Spleen	34.6 nTPM
Lung	30.9 nTPM
Thymus	29.3 nTPM
Stomach	27.4 nTPM
Skin	23.7 nTPM
Kidney	15.6 nTPM
Esophagus	11.8 nTPM

Ciliated cells	23.3 nTPM
Fallopian tube	25.8 nTPM
Endometrium	23.7 nTPM
Lung	22.5 nTPM
Bronchus	21.0 nTPM

Club cells	23.4 nTPM
Prostate	34.3 nTPM
Lung	20.5 nTPM
Bronchus	15.4 nTPM

Dendritic cells	38.6 nTPM
Adipose tissue	59.2 nTPM
PBMC	18.0 nTPM

Endothelial cells	44.9 nTPM
Heart muscle	99.8 nTPM
Skeletal muscle	56.7 nTPM
Vascular	50.5 nTPM
Prostate	50.1 nTPM
Salivary gland	48.3 nTPM
Placenta	46.6 nTPM
Esophagus	46.0 nTPM
Endometrium	45.4 nTPM
Lung	45.3 nTPM
Fallopian tube	42.4 nTPM
Skin	41.1 nTPM
Testis	40.9 nTPM
Tongue	40.8 nTPM
Ovary	39.5 nTPM
Thymus	35.1 nTPM
Breast	28.1 nTPM
Pancreas	25.9 nTPM
Liver	25.2 nTPM

Enteroendocrine cells	22.7 nTPM
Rectum	31.9 nTPM
Small intestine	20.6 nTPM
Colon	15.6 nTPM

Fibroblasts	44.0 nTPM
Fallopian tube	92.8 nTPM
Breast	80.4 nTPM
Skin	64.2 nTPM
Prostate	58.7 nTPM
Salivary gland	50.5 nTPM
Skeletal muscle	48.9 nTPM
Adipose tissue	47.0 nTPM
Esophagus	44.1 nTPM
Vascular	42.8 nTPM
Stomach	34.6 nTPM
Heart muscle	28.2 nTPM
Lung	26.6 nTPM
Placenta	25.8 nTPM
Thymus	24.7 nTPM
Pancreas	18.9 nTPM
Liver	15.4 nTPM

Granulocytes	21.7 nTPM
Lung	23.7 nTPM
Fallopian tube	21.9 nTPM
Tongue	19.4 nTPM

Intestinal goblet cells	21.6 nTPM
Small intestine	34.8 nTPM
Rectum	18.0 nTPM
Colon	12.1 nTPM

Lymphatic endothelial cells	30.0 nTPM
Fallopian tube	38.3 nTPM
Ovary	21.8 nTPM

Macrophages	36.1 nTPM
Adipose tissue	60.8 nTPM
Fallopian tube	48.6 nTPM
Salivary gland	45.1 nTPM
Skeletal muscle	43.8 nTPM
Vascular	42.1 nTPM
Skin	41.2 nTPM
Tongue	39.1 nTPM
Esophagus	38.5 nTPM
Prostate	38.1 nTPM
Stomach	36.0 nTPM
Bone marrow	34.5 nTPM
Thymus	33.8 nTPM
Kidney	31.0 nTPM
Spleen	30.1 nTPM
Endometrium	28.9 nTPM
Testis	27.9 nTPM
Lung	23.0 nTPM
Breast	22.1 nTPM
Pancreas	20.6 nTPM

Basal prostatic cells	29.1 nTPM
Prostate	29.1 nTPM

Basal respiratory cells	14.0 nTPM
Bronchus	14.0 nTPM

Basal squamous epithelial cells	22.8 nTPM
Esophagus	22.8 nTPM

Bipolar cells	32.3 nTPM
Eye	32.3 nTPM

Paneth cells	15.1 nTPM
Small intestine	20.7 nTPM
Rectum	13.8 nTPM
Colon	10.9 nTPM

Plasma cells	37.9 nTPM
Esophagus	46.8 nTPM
Thymus	43.5 nTPM
Spleen	39.9 nTPM
Salivary gland	39.8 nTPM
Fallopian tube	37.3 nTPM
Stomach	35.2 nTPM
Bone marrow	31.7 nTPM
Liver	28.5 nTPM

Schwann cells	45.1 nTPM
Vascular	63.7 nTPM
Esophagus	35.9 nTPM
Adipose tissue	35.5 nTPM

Serous glandular cells	20.4 nTPM
Salivary gland	31.9 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	44.2 nTPM
Endometrium	71.2 nTPM
Adipose tissue	68.6 nTPM
Skin	63.9 nTPM
Tongue	53.6 nTPM
Skeletal muscle	51.5 nTPM
Vascular	50.9 nTPM
Prostate	46.8 nTPM
Fallopian tube	45.3 nTPM
Ovary	44.5 nTPM
Salivary gland	42.3 nTPM
Breast	33.2 nTPM
Lung	30.6 nTPM
Esophagus	30.0 nTPM
Thymus	26.5 nTPM
Liver	25.9 nTPM
Placenta	23.4 nTPM

Suprabasal keratinocytes	20.5 nTPM
Skin	26.8 nTPM
Tongue	14.1 nTPM

T-cells	37.1 nTPM
Esophagus	51.1 nTPM
Adipose tissue	45.6 nTPM
Tongue	43.6 nTPM
Endometrium	43.1 nTPM
Salivary gland	42.9 nTPM
Skeletal muscle	42.0 nTPM
Lymph node	39.6 nTPM
Vascular	39.0 nTPM
Fallopian tube	38.4 nTPM
Bone marrow	37.0 nTPM
Spleen	36.5 nTPM
Skin	35.7 nTPM
Prostate	35.7 nTPM
Kidney	33.7 nTPM
Stomach	32.9 nTPM
Lung	31.7 nTPM
Liver	31.4 nTPM
Thymus	31.4 nTPM
Breast	31.4 nTPM
PBMC	29.3 nTPM
Colon	27.3 nTPM

Undifferentiated cells	20.0 nTPM
Small intestine	21.9 nTPM
Rectum	20.2 nTPM
Colon	17.7 nTPM

Amygdala excitatory	290.3 nTPM
Thalamus	378.0 nTPM
Hypothalamus	367.7 nTPM
Basal ganglia	301.3 nTPM
Amygdala	265.3 nTPM
Cerebral cortex	217.5 nTPM
Hippocampus	212.0 nTPM

Astrocyte	154.2 nTPM
Amygdala	207.5 nTPM
Hypothalamus	183.5 nTPM
Basal ganglia	172.1 nTPM
Thalamus	150.4 nTPM
Cerebral cortex	150.1 nTPM
Hippocampus	149.7 nTPM
Spinal cord	145.1 nTPM
Midbrain	140.8 nTPM
Medulla oblongata	135.0 nTPM
Pons	134.3 nTPM
Cerebellum	128.3 nTPM

Bergmann glia	250.3 nTPM
Cerebellum	269.7 nTPM
Pons	253.2 nTPM
Medulla oblongata	228.0 nTPM

Central nervous system macrophage	256.5 nTPM
Amygdala	330.4 nTPM
Hypothalamus	326.5 nTPM
Basal ganglia	277.2 nTPM
Hippocampus	254.7 nTPM
Thalamus	248.7 nTPM
Midbrain	247.9 nTPM
Cerebral cortex	240.2 nTPM
Pons	229.6 nTPM
Spinal cord	229.3 nTPM
Cerebellum	224.0 nTPM
Medulla oblongata	213.2 nTPM

Cerebellar inhibitory	192.3 nTPM
Spinal cord	206.2 nTPM
Pons	197.9 nTPM
Medulla oblongata	192.4 nTPM
Cerebellum	185.2 nTPM
Midbrain	179.8 nTPM

Cge interneuron	279.2 nTPM
Hypothalamus	351.8 nTPM
Amygdala	317.9 nTPM
Basal ganglia	285.4 nTPM
Hippocampus	279.5 nTPM
Cerebral cortex	253.8 nTPM
Midbrain	246.4 nTPM
Thalamus	219.5 nTPM

Choroid plexus epithelial cell	192.8 nTPM
Basal ganglia	270.7 nTPM
Medulla oblongata	192.2 nTPM
Thalamus	189.1 nTPM
Hippocampus	119.3 nTPM

Committed oligodendrocyte precursor	160.2 nTPM
Hypothalamus	228.7 nTPM
Amygdala	224.4 nTPM
Spinal cord	195.0 nTPM
Thalamus	158.7 nTPM
Cerebral cortex	149.5 nTPM
Basal ganglia	145.6 nTPM
Medulla oblongata	140.7 nTPM
Hippocampus	138.1 nTPM
Pons	133.7 nTPM
Midbrain	133.6 nTPM
Cerebellum	114.2 nTPM

Deep-layer corticothalamic and 6b	409.5 nTPM
Amygdala	450.3 nTPM
Hypothalamus	448.6 nTPM
Midbrain	437.1 nTPM
Hippocampus	434.8 nTPM
Cerebral cortex	380.6 nTPM
Basal ganglia	305.7 nTPM

Deep-layer intratelencephalic	232.6 nTPM
Hypothalamus	271.5 nTPM
Amygdala	239.4 nTPM
Hippocampus	233.3 nTPM
Cerebral cortex	219.8 nTPM
Basal ganglia	198.8 nTPM

Deep-layer near-projecting	328.2 nTPM
Hypothalamus	488.6 nTPM
Basal ganglia	346.8 nTPM
Amygdala	323.3 nTPM
Cerebral cortex	248.5 nTPM
Hippocampus	233.8 nTPM

Eccentric medium spiny neuron	404.6 nTPM
Amygdala	460.6 nTPM
Hippocampus	440.6 nTPM
Thalamus	440.3 nTPM
Cerebral cortex	371.4 nTPM
Basal ganglia	368.7 nTPM
Hypothalamus	346.0 nTPM